rs504508

Variant names:

• chr13-30090862-G-A
• rs504508

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.725 in 152,166 control chromosomes in the GnomAD database, including 40,877 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.72 (40877 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110262 AN: 152048 Hom.: 40860 Cov.: 33

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.739

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.725 AC: 110316 AN: 152166 Hom.: 40877 Cov.: 33 AF XY: 0.714 AC XY: 53111 AN XY: 74386

African (AFR) AF: 0.648 AC: 26898 AN: 41512

American (AMR) AF: 0.678 AC: 10366 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2916 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2050 AN: 5178

South Asian (SAS) AF: 0.720 AC: 3480 AN: 4830

European-Finnish (FIN) AF: 0.641 AC: 6776 AN: 10570

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55155 AN: 67994

Other (OTH) AF: 0.737 AC: 1558 AN: 2114

Alfa AF: 0.792 Hom.: 73331

Bravo AF: 0.718

Asia WGS AF: 0.546 AC: 1904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.72
PhyloP100		-0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs504508; hg19: chr13-30664999;